Presented by Prof. Dr. Constantin Pape (University of Gottingen, Germany) Morphology, gene expression and cellular dynamics are three fundamental observable modalities used to study cells. Recent advances in spatial transcriptomics and microscopy enable joint recording of all three and promise to further our understanding of cellular processes. However, this requires the analysis of large and diverse datasets - a challenging task, especially due to the different foundational methods across communities with expertise in sequence and image analysis. Challenges and solutions to image analysis and visualization for joint transcriptomics and microscopy will be discussed, based on a collaborative project to map the transcriptome during early mouse embryo development.